The Gut-Brain Axis and Migraine: What Your Gut May Be Telling Your Head

By Dr. Suraj Malhan, DO, MS
Headache & Facial Pain Neurologist

We often think of migraine as purely a brain problem—but what if your gut plays just as big a role? Emerging research reveals that the gut-brain axis—the complex communication network between your digestive system and your central nervous system—may be a major player in migraine pathophysiology.

In this post, I’ll break down what the gut-brain axis is, how it affects migraines, and what practical steps you can take to support your gut—and possibly your head.

What Is the Gut-Brain Axis?

The gut and the brain are in constant conversation, connected by biochemical messengers, including the vagus nerve, hormones, neurotransmitters, and immune signals. The enteric nervous system—sometimes called your “second brain”—can influence pain sensitivity, mood, and inflammation.

Your gut microbiota (the trillions of bacteria living in your intestines) produce metabolites like short-chain fatty acids (SCFAs) and tryptophan derivatives that can directly influence your brain’s health and inflammation levels.

Migraine and the Gut: More Connected Than You Think

Over 70% of people with migraine report gastrointestinal (GI) symptoms, including nausea, vomiting, constipation, and reflux. These symptoms often occur during and between attacks.

More strikingly, migraine is associated with multiple GI conditions:

• Irritable Bowel Syndrome (IBS)

• Functional Dyspepsia

• Gastroparesis

• Celiac Disease

• Inflammatory Bowel Disease (IBD)

Research suggests shared mechanisms—such as dysbiosis (gut microbiome imbalance), mitochondrial dysfunction, and altered serotonin signaling—link these disorders to migraine.

What the Research Shows

A 2023 study by Yong et al. analyzed the gut microbiota of individuals with episodic and chronic migraine. The findings? People with migraine had significantly different microbial compositions compared to healthy controls. Certain gut bacteria, such as Agathobacter, were associated with lower headache severity.

Other studies show:

• Gut inflammation can lead to blood-brain barrier permeability (“leaky brain”), worsening neuroinflammation.

• Stress can disrupt the hypothalamic-pituitary-adrenal (HPA) axis, altering both cortisol levels and gut barrier function.

Dietary Strategies for Migraine Relief

Research-backed dietary interventions that may support both gut and brain health include:

1. Ketogenic Diet

• Increases ketone body production

• Supports mitochondrial function

• May protect against neuroinflammation

2. Intermittent Fasting

• Activates cellular repair via autophagy

• Boosts BDNF (Brain-Derived Neurotrophic Factor)

• Enhances mitochondrial biogenesis

3. MIND Diet

• Mediterranean-DASH Intervention for Neurodegenerative Delay

  • Reduces the risk of Alzheimer’s disease

  • Improves memory and slows cognitive decline in stroke survivors

  • Supports mental health, with links to reduced depression and anxiety symptoms

  • May reduce neuroinflammation—a key player in migraine pathophysiology

• Rich in olive oil, berries, leafy greens

4. Fiber-Rich Diets

• Feed beneficial gut bacteria

• Increase SCFA (Short Chain Fatty Acid) production

• Strengthen gut lining and modulate immune response

The Role of Probiotics in Migraine

A 2019 randomized controlled trial (Martami et al., Cephalalgia) showed that a 14-strain probiotic significantly reduced:

• Migraine frequency

• Severity

• Days per month

• Use of abortive medications

Effective strains included:

• Lactobacillus rhamnosus GG (reduces inflammation)

• Bifidobacterium longum (modulates stress)

• Lactobacillus casei (supports serotonin production)

Final Thoughts: Connecting the Dots Between Gut, Brain, and Migraine

Migraine is no longer just a neurological disease confined to the brain—it’s increasingly recognized as a multisystem disorder involving the gut, immune system, and metabolic health.

The gut-brain axis serves as a vital communication highway, where imbalances in gut microbiota (dysbiosis), inflammation, and stress responses can trigger or exacerbate migraine. From altered serotonin production to immune activation, this bidirectional pathway helps explain why many patients with migraine also struggle with gastrointestinal symptoms like nausea, constipation, or IBS.

At the same time, lifestyle interventions—especially dietary changes—offer a powerful, non-pharmacologic way to complement traditional migraine treatments.

Further research is ongoing, but the early data is promising: making migraine easier to stomach might just start with your next meal.

🌱 Key Takeaways:

• A high-fiber, anti-inflammatory diet supports both gut health and migraine prevention by improving microbial diversity and reducing neuroinflammation.

• The MIND diet has strong evidence in protecting against Alzheimer’s disease, cognitive decline, anxiety, and depression, while also supporting brain-gut balance that may ease migraine symptoms.

• Probiotics and prebiotics show promise in modulating the gut microbiome and reducing migraine frequency, intensity, and medication reliance.

• For patients with delayed gastric emptying or nausea during attacks, treatment strategies may need to include non-oral formulations or gut-friendly drug delivery approaches.

Want more evidence-based tips on migraine relief, brain health, and lifestyle strategies that actually work?

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